Engrave, carve, paint, or somehow put unalterable numbers on everything!
Each student has a number & uses that tool (or whatever) each class. No
one leaves the room until you have them lined up numerically - a student
can let you know when they're all there. If they all share something at a
table, then assign table numbers and do the same check at the end of
class. Even if they leave without you finishing inventory, you or a
student can quickly figure out what's missing at the beginning of next
class.
This also stops distructive kids who get pleasure out of breaking or
ruining things.